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Crystal structure of the adduct between human serum transferrin and cisplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 15% w/v PEG 3350, 16% v/v glycerol, 8 mM disodium malonate, and 150 mM Na-PIPES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.81 67.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.34 α = 90 b = 156.4 β = 90 c = 107.44 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.17 102.77 100 1 13.7 12.8 19869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.17 3.22 100 0.8 2.3 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4X1B 3.17 102.77 18841 1028 99.92 0.1808 0.17744 0.1802 0.24316 0.2461 RANDOM 112.79
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 8.94 -0.87 -8.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.946 r_long_range_B_refined 14.064 r_mcangle_it 8.305 r_dihedral_angle_1_deg 6.932 r_scbond_it 6.505 r_mcbond_it 5.154 r_dihedral_angle_2_deg 3.145 r_angle_refined_deg 0.979 r_chiral_restr 0.078 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.946 r_long_range_B_refined 14.064 r_mcangle_it 8.305 r_dihedral_angle_1_deg 6.932 r_scbond_it 6.505 r_mcbond_it 5.154 r_dihedral_angle_2_deg 3.145 r_angle_refined_deg 0.979 r_chiral_restr 0.078 r_gen_planes_refined 0.003 r_bond_refined_d r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5202 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing autoPROC data processing